I started doing the Davidion series on my Captain 3 and was wondering what happened to half the reward choices we had at the end of the missions...

Examples...

Skirmish---The regenerative and covariant shield choice is gone http://www.stowiki.org/Mission:_Skirmish
Spin the Wheel---Poloron Weapons choice is gone http://www.stowiki.org/Mission:_Spin_the_Wheel
What Lies Beneath--Both Armor choices are gone http://www.stowiki.org/Mission:_What_Lies_Beneath
Everything Old is New---Phaser beam array choices are gone(non retrofit) http://www.stowiki.org/Mission:_Everything_Old_is_New